title: sample_121: Liver from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: LMMJ-06-GMP

status: Public on May 16 2024

type: SRA

city: Paris

first: Chloé

last: Arfeuille

address: 48, boulevard Sérurier

country: France

institute: APHP

library_source: transcriptomic

data_processing:
Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 24 -r 150 -g 2 --library-type fr-firststrand). Gene expression was quantified using the full Gencode v26lift37. We used HTSeq (Anders et al., 2015) to obtain the number of reads associated to each gene in the Gencode v26lift37 database (restricted to protein-coding genes, antisense and lincRNAs). Bioconductor DESeq package (Anders and Huber, 2010) was used to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
Assembly: hg19
Supplementary files format and content: FPKM file  in txt format

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
total RNA was extracted from mononuclear cells or sorted HSPC (1000 to 10000 cells) using the RNeasy Mini or Micro Kit (Qiagen).
Libraries were prepared with TruSeq® Stranded Total RNASample preparation kit (Illumina) according to supplier’s recommendations. Briefly the ribosomal RNA fraction was removed from 1μg of total RNA using the Ribo-Zero™ Gold Kit (Epicentre). Fragmentation was then achieved using divalent cations under elevated temperature to obtain approximately 300bp pieces. Double strand cDNA synthesis was performed using reverse transcriptase and random primers, Illumina adapters were ligated and cDNA library was PCR amplified for sequencing. Paired-end 75b sequencing was then carried out on a HiSeq4000 (Illumina).

treatment_protocol: CD34+ cells were selected from mononucleated cells using the Easysep Human CD34 positive selection kit and Easysep magnet (StemCell Technologies, Vancouver, Canada) following the manufacturer's instructions. Cells were phenotyped on a BD FACSCantoTM II analyzer (BD Biosciences) using marker combinations that have been validated in fetal and adult bone marrow (Notta et al., 2011, 2016):  CMP CD34+CD38+CD45RA-CD135+, GMP CD34+CD38+CD45RA+CD135+ and MEP CD34+CD38+CD45RA-CD135- .

tag: tissue

value: Peripheral blood

tag: cell type

value: Sorted  GMP

tag: sample type

value: JMML

tag: jmml patients_unique_identifier

tag: age(wg

value: weeks of_gestation;y:years):0.2 Y

value: No


title: LMMJ-06-CMP

value: Sorted  CMP


title: sample_120: Intestine from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

country: USA

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using fqC v0.11.5 and TrimGalore! software v0.6.4_dev. This software was used to trim low-quality ends from reads, for Illumina adapter removal, and for removal of excess poly(A)-tails.
STAR v2.7.7a was used for alignment of reads to the rainbow trout genome using the default alignment parameters recommended by the STAR software.
Gene counts for reverse-stranded preparations were provided by STAR v2.7.7a using default parameters recommended by the STAR software.
Read counts output from the STAR v2.7.7a software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-BiocManager Release 1.30.10.
Genome_build: All unmasked sequences from the rainbow trout primary assembly in Ensemble (Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly)
Supplementary_files_format_and_content: Tab-delimited text files of effective read counts, rounded to the nearest whole number

molecule: polyA RNA

organism: Oncorhynchus mykiss

source_name: Intestine

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly-A selected kit with 200-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input. Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer. The RNA integrity was checked by Agilent Bioanalyzer 2100 and samples with clean rRNA peaks were used for further experiments.
RNA-Seq of 150 bp PE (paired end) reads were sequenced on Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).

tag: FISH strain

value: VSel

tag: pathogen strain

value: IHNV

tag: time post pathogen challenge

value: 4 hrs

value: Intestine


title: LMMJ-05-GMP

source_name: Bone Marrow

value: Bone Marrow

value: weeks of_gestation;y:years):3.3 Y


title: LMMJ-05-CMP


title: sample_119: Intestine from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: LMMJ-04-MEP

value: Sorted  MEP

value: weeks of_gestation;y:years):1.1 Y


title: LMMJ-03-MEP

value: weeks of_gestation;y:years):1.4 Y


title: LMMJ-04-CMP


title: LMMJ-03-GMP


title: LMMJ-01-MEP

value: weeks of_gestation;y:years):2.7 Y


title: LMMJ-03-CMP


title: sample_115: Intestine from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: LMMJ-01-CMP


title: sample_114: Kidney from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

source_name: Kidney

value: Kidney


title: LMMJ-01-GMP


title: EHRD29-GMP

value: Healthy prenatal

value: weeks of_gestation;y:years):22.2 WG


title: sample_113: Kidney from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: LMMJ-06-MEP

value: Peripheral blood

value: JMML


title: sample_122: Liver from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

source_name: Liver

value: Liver


title: EHRD29-CMP

value: Sorted  CMP

value: No


title: sample_112: Kidney from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: VSel

value: IHNV


title: EHRD23-GMP

value: Sorted  GMP

value: weeks of_gestation;y:years):19 WG


title: LMMJ-05-MEP

value: Bone Marrow

value: weeks of_gestation;y:years):3.3 Y


title: sample_118: Intestine from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: 4 hrs

value: Intestine


title: EHRD23-MEP

value: Sorted  MEP


title: sample_111: Kidney from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: Kidney


title: LMMJ-04-GMP

value: weeks of_gestation;y:years):1.1 Y


title: sample_117: Intestine from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: EHAB72-MEP

value: Healthy prenatal

value: weeks of_gestation;y:years):9.5 WG


title: EHAB72-GMP


title: EHAB72-CMP


title: sample_110: Kidney from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: EHAB69-MEP


title: sample_109: Kidney from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: EHAB69-CMP


title: EHAB63-MEP

value: weeks of_gestation;y:years):11.2 WG


title: sample_108: Liver from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: 0 hrs

value: Liver


title: EHRD29-MEP

value: weeks of_gestation;y:years):22.2 WG

value: No


title: EHAB69-GMP


title: EHAB63-GMP-ARN-1


title: EHAB63-CMP

value: Sorted  CMP


title: sample_107: Liver from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: VSel

value: IHNV


title: sample_116: Intestine from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_106: Liver from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_155

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: tab-delimited text file with filtered raw counts

source_name: head and squamous cell carcinoma

growth_protocol: 134 primary tumors were collected as FFPE specimens from surgically resected tumor tissues or pan-endoscopic biopsies.

extract_protocol:
Simultaneous DNA and total RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD using unique dual indexing

treatment_protocol: Serial sections of FFPE tumor blocks were macrodissected for the enrichment of tumor cells.

value: head and squamous cell carcinoma

value: tumor tissue

tag: hpv-status

value: positive

tag: mps-all

tag: mps-hpv negative


title: sample_105: Liver from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: EHRD23-CMP

value: Bone Marrow

value: weeks of_gestation;y:years):19 WG


title: HNSCC_LMU_KKG_Sample_147

value: negative


title: HNSCC_LMU_KKG_Sample_157


title: H520_T5_BaP

city: Rockville

first: Jiyeon

last: Choi

state: Maryland

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

data_processing:
Illumina Casava1.7 software was used for basecalling and the BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
The number of reads (R1) completely matching 12bp barcode sequences (tag counts) plus 3bp adjacent spacer sequences were counted
Tag counts were converted to tag counts per million reads (TPM) for each sample and DNA input
A pseudo count of 1 was added to TPM of each tag (adjusted TPM). Adjusted TPM of each tag from each sample was normalized to adjusted TPM from DNA input to obtain normalized expression levels of each tag
A549_T1, T2, T3, T4, and T5 BaP and DMSO were normalized to A549_Input_v1; H520_T1, T2, T3, T4, and T5 BaP and DMSO were normalized to H520_Input_v2
Supplementary files format and content: Tag abundance measurements are included in *_count_TPM.txt files with column headings of Tag:15bp tag sequence, strand: minus strand, Depth: count of the reads matching the 15bp tag sequence, TotalCount: total read counds of the sample matching any tag sequence, TPM: Depth normalized over the TotalCount times one million

extract_protocol:
Total RNA was isolated using Qiagen RNeasy kit, and mRNA was subsequently isolated using PolyA purist MAG kit.
cDNA was synthesized from mRNA using Superscript III reverse transcriptase, from which short sequences encompassing 12 bp unique tags were amplified using Q5 high-fidelity polymerase and primers introducing Illumina TruSeq adapter sequences.

treatment_protocol: Exposure to 10 µM BaP for 18 h and 42 h in A549 and H520, respectively

tag: cell line

value: Lung squamous cell carcinoma cell line

tag: treatment

value: BaP


title: sample_104: Liver from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_103: Liver from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_151


title: H520_T5_DMSO

value: DMSO


title: H520_T4_BaP


title: HNSCC_LMU_KKG_Sample_152


title: HNSCC_LMU_KKG_Sample_153


title: HNSCC_LMU_KKG_Sample_146


title: H520_T4_DMSO


title: HNSCC_LMU_KKG_Sample_150


title: sample_101: Intestine from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: Intestine


title: HNSCC_LMU_KKG_Sample_145


title: HNSCC_LMU_KKG_Sample_148


title: HNSCC_LMU_KKG_Sample_144


title: HNSCC_LMU_KKG_Sample_149


title: H520_T3_BaP


title: HNSCC_LMU_KKG_Sample_142


title: H520_T3_DMSO


title: HNSCC_LMU_KKG_Sample_154


title: sample_100: Intestine from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: 0 hrs


title: sample_099: Intestine from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_141


title: HNSCC_LMU_KKG_Sample_140


title: H520_T2_BaP


title: HNSCC_LMU_KKG_Sample_139


title: sample_098: Intestine from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_138


title: sample_102: Intestine from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_137


title: HNSCC_LMU_KKG_Sample_136


title: HNSCC_LMU_KKG_Sample_135


title: sample_096: Kidney from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: Kidney


title: H520_T1_DMSO


title: H520_T1_BaP


title: HNSCC_LMU_KKG_Sample_132


title: sample_097: Intestine from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_143


title: HNSCC_LMU_KKG_Sample_131


title: HNSCC_LMU_KKG_Sample_130


title: A549_T5_BaP

value: Lung adenocarcinoma cell line


title: sample_095: Kidney from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: H520_Input_v2

library_source: genomic

molecule: genomic DNA

source_name: DNA construct

value: DNA construct


title: HNSCC_LMU_KKG_Sample_129


title: sample_094: Kidney from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: H520_T2_DMSO


title: sample_093: Kidney from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: A549_T5_DMSO


title: HNSCC_LMU_KKG_Sample_125


title: HNSCC_LMU_KKG_Sample_124


title: sample_091: Kidney from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: A549_T4_BaP


title: HNSCC_LMU_KKG_Sample_123


title: A549_T4_DMSO


title: HNSCC_LMU_KKG_Sample_122


title: sample_090: Liver from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: NVSel

value: 48 hrs

value: Liver


title: HNSCC_LMU_KKG_Sample_134

value: head and squamous cell carcinoma


title: A549_T3_BaP


title: HNSCC_LMU_KKG_Sample_121

value: tumor tissue


title: A549_T3_DMSO


title: HNSCC_LMU_KKG_Sample_120

value: positive


title: HNSCC_LMU_KKG_Sample_119


title: HNSCC_LMU_KKG_Sample_128


title: sample_092: Kidney from VSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: VSel

value: IHNV


title: HNSCC_LMU_KKG_Sample_127

value: negative


title: sample_088: Liver from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_118


title: A549_T2_BaP


title: HNSCC_LMU_KKG_Sample_117


title: sample_087: Liver from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_126


title: HNSCC_LMU_KKG_Sample_113


title: sample_086: Liver from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: A549_T2_DMSO


title: HNSCC_LMU_KKG_Sample_115


title: sample_085: Liver from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_114


title: A549_T1_DMSO


title: HNSCC_LMU_KKG_Sample_112


title: A549_T1_BaP


title: HNSCC_LMU_KKG_Sample_111


title: HNSCC_LMU_KKG_Sample_108


title: sample_089: Liver from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_084: Intestine from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: A549_Input_v1


title: HNSCC_LMU_KKG_Sample_106


title: sample_083: Intestine from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_105


title: Calu3 cells - Andes virus + 6AZA - 48hrs - rep 3 (Drug study) [Sample 46_AA-3]

city: Los Angeles

first: ARJIT VIJEY

last: JEYACHANDRAN

address: Tiverton Ave

institute: UCLA

data_processing:
Illumina reads from all the samples were mapped to human reference genome by STAR v2.7.9a and read counts per gene were quantified using human genome GRCh38.107 GTF file to generate raw reads counts. Differential expression analysis was performed using DESeq2 v1.34.0 in R v4.1.2
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Calu3 cells

growth_protocol: Cells were cultured in EMEM+15% FBS+1% Pen-Strep+1% MEM NEAA+1% L-glutamine

extract_protocol:
Samples were harvested in TriZol and RNA was extracted using the BioRad RNA Mini kit
Libraries were prepared with KAPA Stranded mRNA-Seq Kit followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand.  cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: Three types of cells described above were either uninfected or infected with ANDV, SNV and HTNV and treated or un-treated with drugs at 48 hrs

value: Infected and Treated


title: HNSCC_LMU_KKG_Sample_104


title: sample_082: Intestine from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: Calu3 cells - Andes virus + 6AZA - 48hrs - rep 2 (Drug study) [Sample 45_AA-2]


title: HNSCC_LMU_KKG_Sample_103


title: HNSCC_LMU_KKG_Sample_100


title: sample_080: Intestine from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_101


title: sample_081: Intestine from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_099


title: HNSCC_LMU_KKG_Sample_097


title: HNSCC_LMU_KKG_Sample_096


title: HNSCC_LMU_KKG_Sample_098


title: Calu3 cells - Andes virus + Favipiravir - 48hrs - rep 2 (Drug study) [Sample 42_AF-3]


title: sample_079: Intestine from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_116


title: sample_078: Kidney from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_038


title: HNSCC_LMU_KKG_Sample_005


title: HNSCC_LMU_KKG_Sample_006


title: Calu3 cells - Andes virus + Favipiravir - 48hrs - rep 1 (Drug study) [Sample 41_AF-2]


title: Calu3 cells - Andes virus + Silymarin - 48hrs - rep 3 (Drug study) [Sample 40_AS-4]


title: HNSCC_LMU_KKG_Sample_027


title: HNSCC_LMU_KKG_Sample_036


title: HNSCC_LMU_KKG_Sample_102


title: Calu3 cells - Andes virus + 6AZA - 48hrs - rep 1 (Drug study) [Sample 44_AA-1]


title: sample_076: Kidney from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: Calu3 cells - Andes virus + Silymarin - 48hrs - rep 2 (Drug study) [Sample 39_AS-3]


title: HNSCC_LMU_KKG_Sample_003


title: Calu3 cells - Andes virus + Favipiravir - 48hrs - rep 3 (Drug study) [Sample 43_AF-4]


title: sample_075: Kidney from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: TET2-KO_B16-OVA_VC_4-2_Biol Rep 3

city: Chapel Hill

first: Meng

last: Cheng

state: NC

address: 107 Pinegate Cir, Apt 9

department: Lineberger Cancer Center

institute: UNC-CH

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
QC analysis steps were performed using the Seurat R package.
We filtered out cells with less than 500 genes per cell, with more than 30% mitochondrial read content, and with less than 5% ribosomal content
The downstream analysis was performed with LIGER with steps including log2-normalization, identification of highly variable genes across cells, dimension reduction with UMAP, louvain clustering, and the discovery of differentially expressed cell-type markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Melanoma

growth_protocol: WT or TET2-KO B16-OVA cells were cultured to 80% confluent in DMEM medium+10% FBS supplemented with pen/strep; and then digested with trypsin to make singe cell suspensions. Then, 2X10^5 cells/mouse suspended in PBS were transplanted to syngeneic C57BL/6 mice at their right flank site s.c.

extract_protocol:
After treatment, WT or TET2-KO B16 tumor tissue were harvested and digested with Collagenase + DNAase to make single cell suspensions in DMEM medium. 10,000 single cells fromt these tumors were isolated for single-cell sequencing under 10X genomics platform.
RNA libraries for RNA-seq were prepared using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics)  and the Illumina NextSeq2000 system was used for sequencing following manufacturer's protocols.

treatment_protocol: PBS or 1g/kg Vitamin C were givein daily through I.V. injection, 100uL each mouse starting at 7 days after inoculation for 2 weekes.

value: Melanoma

value: Mouse Melanoma Cell

tag: genotype

value: TET2 Knockout

value: Vitamin C


title: Calu3 cells - Andes virus + Silymarin - 48hrs - rep 1 (Drug study) [Sample 38_AS-2]


title: HNSCC_LMU_KKG_Sample_032


title: Calu3 cells - Andes virus + Urolithin B - 48hrs - rep 3 (Drug study) [Sample 37_AUB-4]


title: TET2-KO_B16-OVA_VC_4-1_Biol Rep 2


title: sample_073: Kidney from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: Kidney


title: sample_074: Kidney from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: HNSCC_LMU_KKG_Sample_069


title: HNSCC_LMU_KKG_Sample_059


title: sample_072: Liver from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: 24 hrs


title: Calu3 cells - Andes virus + Urolithin B - 48hrs - rep 1 (Drug study) [Sample 35_AUB-2]


title: sample_077: Kidney from NVSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: Calu3 cells - Andes virus + Urolithin B - 48hrs - rep 2 (Drug study) [Sample 36_AUB-3]


title: HNSCC_LMU_KKG_Sample_004


title: sample_071: Liver from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Calu3 cells - Andes virus - 48hrs - rep 3 (Drug study) [Sample 34_AV-3]

value: Infected


title: HNSCC_LMU_KKG_Sample_066


title: sample_070: Liver from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: NVSel


title: TET2-KO_B16-OVA_PBS_3-1_Biol Rep 2

value: PBS


title: HNSCC_LMU_KKG_Sample_077


title: TET2-KO_B16-OVA_PBS_3-0_Biol Rep 1


title: Calu3 cells - Andes virus - 48hrs - rep 2 (Drug study) [Sample 33_AV-2]


title: WT_B16-OVA_VC_2-2_Biol Rep 3

value: WT


title: HNSCC_LMU_KKG_Sample_031

value: head and squamous cell carcinoma


title: sample_069: Liver from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Liver


title: Calu3 cells - Mock - 48hrs - rep 3 (Drug study) [Sample 31_AM-4]

value: Mock


title: HNSCC_LMU_KKG_Sample_028

value: tumor tissue

value: positive


title: sample_067: Liver from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: IHNV


title: sample_068: Liver from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: TET2-KO_B16-OVA_VC_4-0_Biol Rep 1


title: TET2-KO_B16-OVA_PBS_3-2_Biol Rep 3


title: WT_B16-OVA_VC_2-0_Biol Rep 1


title: Calu3 cells - Mock - 48hrs - rep 2 (Drug study) [Sample 30_AM-2]


title: Cardiomyocytes cells - Hantaan virus - 48hrs - rep 2 [Sample 28_V12]

source_name: Cardiomyocytes cells

value: Cardiomyocytes


title: HNSCC_LMU_KKG_Sample_057


title: HNSCC_LMU_KKG_Sample_048

value: negative


title: sample_065: Intestine from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Intestine


title: HNSCC_LMU_KKG_Sample_056


title: Calu3 cells - Mock - 48hrs - rep 1 (Drug study) [Sample 29_AM-1]


title: sample_063: Intestine from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: HNSCC_LMU_KKG_Sample_054


title: Calu3 cells - Andes virus - 48hrs - rep 1 (Drug study) [Sample 32_AV-1]


title: d1759c

city: Mississippi State

first: Hossam

last: Abdelhamed

address: Wise drive

institute: CVM

description:
FPKM.xls
d1759vsWT_deg_all

data_processing:
CLC Genomic Workbench 24.0.1
Clean sequence reads were obtained by triming reads containing adapter and removing poly-N sequence and reads with low-quality
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of the reference genome and aligning clean reads to reference genome were used on Bowtie2
Raw reads were filtered by (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); and (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
The RNA-seq reads were assembled according to the reference genomes using Rockhopper(R. McClure, et al, 2013)
Assembly: AE017262.2
Supplementary files format and content: d1031vsWT_deg_all.xls: differentially expressed genes
Supplementary files format and content: d1759vsWT_deg_all.xls: differentially expressed genes

organism: Listeria monocytogenes serotype 4b str. F2365

source_name: Bacteria cells

growth_protocol: Listeria monocytogenes F2365 (n=6) were cultured overnight and were diluted 1:10 in BHI and incubated at 37 °C with shaking for ~1 h to reach OD600 ~ 0.2-0.3

extract_protocol:
Total RNA was extracted using the FastRNA spin kit for microbes and the FastPrep-24 instrument (MP Biomedicals, Santa Ana, CA) following manufacturer's instruction
Library construction and sequencing was performed by Novogen

treatment_protocol: Three replicates each of (1) WT (2)d1031 and (3) d1759 were treated with 8 mM Hydrogen peroxide

value: Bacteria cells

value: gltC mutant strain

value: 8 mM Hydrogen peroxide treatment


title: WT_B16-OVA_PBS_1-1_Biol Rep 2

value: Melanoma

value: Mouse Melanoma Cell


title: WT_B16-OVA_PBS_1-2_Biol Rep 3


title: HNSCC_LMU_KKG_Sample_055


title: sample_064: Intestine from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: NVSel

value: 24 hrs


title: WT_B16-OVA_PBS_1-0_Biol Rep 1

value: WT

value: PBS


title: Cardiomyocytes cells - Hantaan virus - 48hrs - rep 1 [Sample 27_V10]

value: Infected


title: d1759b

description:
FPKM.xls
d1759vsWT_deg_all


title: WT_B16-OVA_VC_2-1_Biol Rep 2

value: Vitamin C


title: Cardiomyocytes cells - Andes virus - 48hrs - rep 1 [Sample 25_V8]


title: Cardiomyocytes cells - Andes virus - 48hrs - rep 2 [Sample 26_V9]


title: HNSCC_LMU_KKG_Sample_033

value: head and squamous cell carcinoma

value: tumor tissue


title: sample_062: Intestine from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: IHNV


title: sample_061: Intestine from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: d1759a

description:
FPKM.xls
d1759vsWT_deg_all


title: sample_066: Intestine from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Cardiomyocytes cells - Sin Nombre virus - 48hrs- rep 2 [Sample 24_V5]

value: Cardiomyocytes


title: HNSCC_LMU_KKG_Sample_019

value: negative


title: sample_060: Kidney from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Kidney


title: WTc

description:
FPKM.xls
d1031vsWT_deg_all
d1759vsWT_deg_all

value: Bacteria cells


title: sample_059: Kidney from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Cardiomyocytes cells - Mock - 48hrs - rep 2 [Sample 22_V3]

value: Mock


title: WTb

value: 8 mM Hydrogen peroxide treatment


title: HNSCC_LMU_KKG_Sample_018

value: positive


title: WTa


title: sample_058: Kidney from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Cardiomyocytes cells - Mock - 48hrs - rep 1 [Sample 21_V2]


title: HNSCC_LMU_KKG_Sample_044


title: sample_057: Kidney from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_056: Kidney from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Astrocytes cells - Hantaan virus - 48hrs - rep 2 [Sample 19_AS23]

source_name: Astrocytes cells

value: Astrocytes


title: d1031c

description:
FPKM.xls
d1031vsWT_deg_all

value: ccpC mutant strain


title: HNSCC_LMU_KKG_Sample_014


title: sample_055: Kidney from NVSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: NVSel

value: 24 hrs


title: HNSCC_LMU_KKG_Sample_072


title: Astrocytes cells - Hantaan virus - 48hrs - rep 1 [Sample 18_AS22]


title: Astrocytes cells - Hantaan virus - 48hrs - rep 3 [Sample 20_AS24]


title: sample_054: Liver from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs

value: Liver


title: d1031a

description:
FPKM.xls
d1031vsWT_deg_all


title: HNSCC_LMU_KKG_Sample_080


title: Astrocytes cells - Andes virus - 48hrs - rep 3 [Sample 17_AS21]

value: Infected


title: HNSCC_LMU_KKG_Sample_008

value: head and squamous cell carcinoma


title: sample_053: Liver from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: d1031b

description:
FPKM.xls
d1031vsWT_deg_all


title: Cardiomyocytes cells - Sin Nombre virus - 48hrs - rep 1 [Sample 23_V4]


title: EC, tie1 Homo, replicate 1, RNAseq

city: Suita

first: Hiroyuki

last: Nakajima

state: Osaka

address: 6-1 Kishibeshinmachi

department: Department of Cell Biology

country: Japan

institute: National Cerebral and Cardiovascular Center Research Institute

description: RNAseq_tie1 Homo-1_EC

data_processing:
RNA-Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1, and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4.
Assembly: GRCz 11
Supplementary files format and content: Excel CSV files include transcripts per million (TPM) for each sample.

organism: Danio rerio

source_name: homozygous tie1 mutant embryos

extract_protocol:
Trunk and tail region from 47 hpf Tg(kdrl:EGFP);Tg(lyve1:DsRed) tie1-/- zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. After washed in E3 media, samples were incubated with 1 ml of lysis solution containing collagenase P (Roche) and TrypLE Express Enzyme (Gibco) for 20 minutes under occasional pipetting. The dissociated cells in suspension medium (phenol red free DMEM with 1% FBS, 0.8 mM calcium chloride, 50 U/ml penicillin, and 0.05 mg/ml streptomycin) were subjected to cell sorting using a FACS Aria III cell sorter (BD Bioscience). EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1-/- embryos and their tie1+/? siblings using the NucleoSpin XS kit (Macherey-Nagel, 740902.50) according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, 634888).
Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760)

value: Trunk and Tail

value: Endothelial cells


title: HNSCC_LMU_KKG_Sample_050

value: tumor tissue


title: Astrocytes cells - Andes virus - 48hrs - rep 2 [Sample 16_AS20]


title: HNSCC_LMU_KKG_Sample_074

value: negative


title: EC, tie1 Homo, replicate 2, RNAseq

description: RNAseq_tie1 Homo-2_EC


title: sample_052: Liver from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: IHNV


title: Astrocytes cells - Andes virus - 48hrs - rep 1 [Sample 15_AS19]


title: EC, tie1 WT/Het, replicate 2, RNAseq

description: RNAseq_tie1 WT/Het-2_EC

source_name: wild-type and heterozygous siblings


title: HNSCC_LMU_KKG_Sample_012


title: sample_051: Liver from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: HNSCC_LMU_KKG_Sample_001


title: EC, tie1 WT/Het, replicate 1, RNAseq

description: RNAseq_tie1 WT/Het-1_EC


title: sample_050: Liver from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Astrocytes cells - Sin Nombre virus - 48hrs - rep 3 [Sample 14_AS18]


title: Astrocytes cells - Sin Nombre virus - 48hrs - rep 2 [Sample 13_AS17]


title: sample_049: Liver from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: 12568_ID_Cfa6.66_ins_BioRep3

city: Princeton

first: Dhriti

last: Tandon

state: New Jersey

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed to remove barcodes and reads with a qulaity cutoff score of greater than 20 (q>20) were reatined using Trim Galore v0.0.6
ChIP-seq reads were aligned to the canfam3 genome using Bowtie version 1.1.2. Only uniquely mapping reads with distinctive "unqiue molecular identifier" sequences were retained.
To create ChIP-seq coverage plots, we used deeptools v3.5.1 and normalized all libraries to the largest library size. ChIP-seq reads were extended 100bp.
Peaks were called uing MACS v2.2.0 with the significance cut-off q-value <=0.05 and 0.1 for E2F1 and H3K27ac Chip libraries, respectively.
Bigwig files were generated in deeptools v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2.2.0. broadPeak files were generated with MACS v2.2.0, with the q cutoff as 0.1 and --broad-cutoff as 0.1.
Assembly: canFam3.1
Supplementary files format and content: bigWig, narrowPeak/broadPeak (except for Input sample)

organism: Canis lupus familiaris

source_name: Brainstem

extract_protocol:
We extracted nuclei from flash frozen brainstem tissue using the Active Motif High sensitivity kit (Active Motif). Briefly, we re-suspended 50mg of flash-frozen tissue in Tissue fixation solution (4.35ml Molecular grade water, 0.5ml Active Motif 10x PBS, and 140ul 37% (v/v) formaldehyde). We rotated the tube for 8 minutes, added 51.5ul of Active Motif Stop Solution, and followed by 5 minutes of rotation.
ChIP-seq libraries were prepared using the Active Motif High sensitivity kit  complemented with the Active Motif Next Gen DNA library Prep kit and Active Motif Next Gen Indexing kit with 15 PCR cycles. 1 ng of DNA was used as starting material for input and ip samples. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: ins

value: Brainstem

tag: chip antibody

value: input


title: 12558_ID_Cfa6.66_noins_BioRep3

value: noins


title: HNSCC_LMU_KKG_Sample_076


title: 12554_ID_Cfa6.66_noins_BioRep2


title: HNSCC_LMU_KKG_Sample_043


title: Astrocytes cells - Sin Nombre virus - 48hrs - rep 1 [Sample 12_AS16]

value: Astrocytes


title: sample_048: Intestine from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: Intestine


title: HNSCC_LMU_KKG_Sample_015


title: Astrocytes cells - Mock - 48hrs - rep 3 [Sample 11_AS15]

value: Mock


title: sample_047: Intestine from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: NVSel


title: 12552_ID_Cfa6.66_noins_BioRep1


title: Astrocytes cells - Mock - 48hrs - rep 2 [Sample 10_AS14]


title: Astrocytes cells - Mock - 48hrs - rep 1 [Sample 9_AS13]


title: HNSCC_LMU_KKG_Sample_073

value: positive


title: 12527_ID_Cfa6.66_ins_BioRep2


title: HNSCC_LMU_KKG_Sample_060


title: 12517_ID_Cfa6.66_ins_BioRep1


title: Calu3 cells - Hantaan virus - 48hrs - rep 2 [Sample 8_CA18]


title: HNSCC_LMU_KKG_Sample_078


title: sample_046: Intestine from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs


title: sample_044: Intestine from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: 12568_H3K27ac_Cfa6.66_ins_BioRep3

value: H3K27ac (Active Motif; cat# 39034; concentration 1ug/ul)


title: Calu3 cells - Hantaan virus - 48hrs - rep 1 [Sample 7_CA17]

value: Infected


title: HNSCC_LMU_KKG_Sample_075

value: head and squamous cell carcinoma


title: Calu3 cells - Andes virus - 48hrs - rep 2 [Sample 6_CA16]


title: sample_043: Intestine from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: 12558_H3K27ac_Cfa6.66_noins_BioRep3


title: HNSCC_LMU_KKG_Sample_079


title: sample_042: Kidney from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: Kidney


title: Calu3 cells - Andes virus - 48hrs - rep 1 [Sample 5_CA15]


title: HNSCC_LMU_KKG_Sample_061

value: tumor tissue


title: sample_041: Kidney from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Calu3 cells - Sin Nombre virus - 48hrs- rep 2 [Sample 4_CA14]


title: HNSCC_LMU_KKG_Sample_021

value: negative


title: 12527_H3K27ac_Cfa6.66_ins_BioRep2


title: 12552_H3K27ac_Cfa6.66_noins_BioRep1


title: HNSCC_LMU_KKG_Sample_020


title: sample_039: Kidney from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: IHNV


title: sample_045: Intestine from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Calu3 cells - Sin Nombre virus - 48hrs - rep 1 [Sample 3_CA13]


title: Calu3 cells - Mock - 48hrs - rep 2 [Sample 2_CA11]


title: HNSCC_LMU_KKG_Sample_070


title: 12517_H3K27ac_Cfa6.66_ins_BioRep1

value: ins


title: sample_038: Kidney from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Calu3 cells - Mock - 48hrs - rep 1 [Sample 1_CA10]


title: 12568_E2F1_Cfa6.66_ins_BioRep3

value: Brainstem

value: E2F1 (Cell Signalling Technologies; cat# 3742S, Lot 8; concentration 48ug/ml)


title: HNSCC_LMU_KKG_Sample_011


title: sample_037: Kidney from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_036: Liver from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: 4 hrs

value: Liver


title: 12554_H3K27ac_Cfa6.66_noins_BioRep2

value: noins


title: sample_035: Liver from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: HNSCC_LMU_KKG_Sample_037


title: 12558_E2F1_Cfa6.66_noins_BioRep3


city: taipei

first: Jiun-I

last: Lai

state: State...

address: no 155, linong street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming Chiao-Tung University

description:
MB231_cinvin_1
MDA-MB-231 treated with cisplatin/vinorelbine repeat 1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using HISAT2 software (v 2.1.0) (parameters- default)
Read count extraction  were performed using FeatureCounts (v 2.0.0 )
Normalization were performed using DEGseq (v 1.40.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: MDA-MB-231 were treated with DMEM medium,   supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Isolate Kit (NovelGene). 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer's protocols.

treatment_protocol: cells were treated with 7μM cisplatin + 14μM vinorelbine for 24 hours

value: triple negative breast cancer cell line

value: romidepsin


title: MDA-MB-231 treated with DMSO repeat 2

description:
MB231_DMSO_2
MDA-MB-231 treated with DMSO repeat 2

value: DMSO


title: HNSCC_LMU_KKG_Sample_041


title: HNSCC_LMU_KKG_Sample_026


title: sample_034: Liver from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: NVSel


title: MDA-MB-231 treated with DMSO repeat 1

description:
MB231_DMSO_1
MDA-MB-231 treated with DMSO repeat 1


title: HNSCC_LMU_KKG_Sample_010

value: positive


title: 12517_E2F1_Cfa6.66_ins_BioRep1


title: sample_040: Kidney from NVSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs


title: HNSCC_LMU_KKG_Sample_029

value: head and squamous cell carcinoma


title: sample_032: Liver from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: si-Robo4-transfected and TNFα-treated HUVECs no3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description:
siRobo4_TNF_ex3
TPM_for_GEO_upload_COX2.txt

data_processing:
Sequencing was performed on an Illumina NextSeq550 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs; Lonza) were cultured in EGM-2-MV medium (Lonza).

extract_protocol:
The cells were used for total RNA preparation using RNeasy Mini Kit (Qiagen).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: siRNA for Robo4 (SI03066896), β-catenin (SI00029750) and their control (AllStars Negative Control) were purchased from Qiagen. siRNA sequences are shown in Table S1. For knockdown experiments, HUVECs (2.0×10^5 cells) were transfected with siRNA (25 pmol) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and cultured in EBM-2 (Lonza) containing 0.5% FBS for 20 h. The resulting cells were then stimulated with TNFα (1 µg/ml) for 6 h.

value: HUVECs

value: human umbilical vein endothelial cells

value: wild type

value: si-Robo4 transfected/TNFα treated

tag: time

value: 26 hours


title: HNSCC_LMU_KKG_Sample_046

value: tumor tissue


title: H1[rAPOBEC1]  replicate 1

city: Haining

first: Huanchang

last: Tu

address: 718 East Haizhou Rd., Haining, Zhejiang

country: China

institute: Zhejiang University

description: the processed file is only for this sample

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQformat, which contains sequence information and corresponding sequencing quality information.
The raw data was accessed with FastQC (v0.11.9) for overall quality of the bulk RNA-seq fastq files, identifying any potential issues.
Paired-end sequencing was performed on the Bulk RNA-seq libraries, and the resulting reads were trimmed using cutadapt (v4.1).
Trimmed reads were mapped to the hg38 assembly with bowtie2 (v2.4.5), sorted with samtools (v1.6) and quantified against Gencode (v41) annotations using featureCounts (v2.0.1).
Assembly: hg38
Supplementary files format and content: txt files: counts of the samples
Supplementary files format and content: csv file: the matrix of counts for samples

source_name: hESC

extract_protocol:
Total RNA was extracted from hESCs with the Trizol reagent (Thermo, 15596026) according to the manufacturer's instructions.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system(Agilent，USA) and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

value: hESC

value: human embryonic stem cells

value: tetON-rAPOBEC

value: With doxycyclin for 24 hours


title: sample_031: Liver from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: IHNV

value: 4 hrs

value: Liver


title: si-Robo4-transfected and TNFα-treated HUVECs no2

description:
siRobo4_TNF_ex2
TPM_for_GEO_upload_COX2.txt


description:
MB231_cinvin_2
MDA-MB-231 treated with cisplatin/vinorelbine repeat 2

value: triple negative breast cancer cell line

value: romidepsin


title: 12554_E2F1_Cfa6.66_noins_BioRep2

value: noins

value: Brainstem

value: E2F1 (Cell Signalling Technologies; cat# 3742S, Lot 8; concentration 48ug/ml)


title: sample_030: Intestine from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: NVSel

value: Intestine


title: AND2 hCOs 45 days scRNAseq

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

description: 10x Genomics

data_processing:
Raw scRNA-seq output was processed in order to generate a count matrix with CellRanger Count (version 6.1.2. 10X Genomics)
Assembly: GRCh38 human reference genome
Supplementary files format and content: Tab-separated values files and Matrix files

source_name: hCOs from Human Embryonic Stem Cell (hESCs)

extract_protocol:
hCOs were collected with the aid of a pipette and treated with HBSS (Hank's Balanced Salt Solution; 1X, Gibco, #14180046) for 15 minutes. The organoid were centrifuged (3 minutes at 600 rpm) and digested with trypsin (0.025%, Gibco) for 20 minutes at 37°C and trypsin inhibition with 1:1 DMEM:F12 + 10% FBS. Subsequently, the dissociated and individual cells were centrifuged (3 minutes at 600 rpm) and resuspended in a buffered solution of BSA (0.04%, Sigma) in PBS at 4°C.
The single cell library was prepared according to manufacturer’s instructions using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) workflow by the Genomics Unit of the Instituto de Salud Carlos III

value: AND-2 cell line

tag: age

value: 45 days of culture


title: si-Robo4-transfected and TNFα-treated HUVECs no1

description:
siRobo4_TNF_ex1
TPM_for_GEO_upload_COX2.txt

value: HUVECs

value: human umbilical vein endothelial cells

value: wild type

value: si-Robo4 transfected/TNFα treated

value: 26 hours


title: 12552_E2F1_Cfa6.66_noins_BioRep1


title: si-Robo4-transfected HUVECs no3

description:
siRobo4_ex3
TPM_for_GEO_upload_COX2.txt

value: si-Robo4 transfected


title: HNSCC_LMU_KKG_Sample_009

tag: tissue

value: head and squamous cell carcinoma

value: tumor tissue

value: positive


title: SHH-MB_PDX1, THZ531, 16h, rep1

city: Shanghai

first: Yi

last: Sui

address: South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description:
160944_T5311_1
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

data_processing:
Trim galore was used to automatically detect and trim adapters.
Reads were mapped to GRCh38 or GRCm38 reference genome using Hisat2.
Counts were generated using HTSeq (version 0.11.1).
Assembly: hg38 for Homo sapiens samples, mm10 for Mus musculus samples.
Supplementary files format and content: txt files included raw counts and FPKM for each Sample

source_name: Cells freshly constructed from SHH-subtype medulloblastoma patient-derived xenograft

extract_protocol:
Cells treated with corresponding small molecular inhibitors and mouse cerebellum tissues were harvested and lysed in Trizol. Samples for RNA-seq assays were then sent to MAJORBIO company (Shanghai, China) for RNA extraction.
Samples for RNA-seq assays were sent to MAJORBIO company (Shanghai, China) for library construction and second-generation sequencing.

tag: cell type

value: human SHH-subtype medulloblastoma cells

value: 1μM THZ531 treated for 16h


title: sample_033: Liver from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: IHNV

value: 4 hrs

value: Liver


title: 12527_E2F1_Cfa6.66_ins_BioRep2

value: ins

value: Brainstem

value: E2F1 (Cell Signalling Technologies; cat# 3742S, Lot 8; concentration 48ug/ml)


title: HNSCC_LMU_KKG_Sample_017

value: negative


title: SHH-MB_PDX1, THZ531, 16h, rep2

description:
160944_T5311_2
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

value: Cells freshly constructed from SHH-subtype medulloblastoma patient-derived xenograft


title: SHH-MB_PDX1, AZD4573, 16h, rep2

description:
160944_AZD01_2
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

value: 0.1μM AZD4573 treated for 16h


title: sample_028: Intestine from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

source_name: Intestine

value: NVSel

value: Intestine


title: si-Robo4-transfected HUVECs no1

description:
siRobo4_ex1
TPM_for_GEO_upload_COX2.txt

value: HUVECs

value: human umbilical vein endothelial cells

value: wild type

value: si-Robo4 transfected

value: 26 hours


title: H1[rAPOBEC1]  replicate 2

value: hESC

value: human embryonic stem cells

value: tetON-rAPOBEC

value: With doxycyclin for 24 hours


title: sample_029: Intestine from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: IHNV

value: 4 hrs


title: si-Robo4-transfected HUVECs no2

description:
siRobo4_ex2
TPM_for_GEO_upload_COX2.txt


title: sample_026: Intestine from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: SHH-MB_PDX1, AZD4573, 16h, rep1

description:
160944_AZD01_1
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

value: human SHH-subtype medulloblastoma cells


title: HNSCC_LMU_KKG_Sample_040

value: head and squamous cell carcinoma

value: tumor tissue

value: positive


title: HNSCC_LMU_KKG_Sample_063

value: negative


title: si-control-transfeced and TNFα-treated HUVECs no3

description:
siCont_TNF_ex3
TPM_for_GEO_upload_COX2.txt

value: TNFα treated


title: HNSCC_LMU_KKG_Sample_042


title: SHH-MB_PDX1, THZ1, 16h, rep2

description:
160944_T101_2
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

value: Cells freshly constructed from SHH-subtype medulloblastoma patient-derived xenograft

value: 0.1μM THZ1 treated for 16h


title: si-control-transfeced and TNFα-treated HUVECs no2

description:
siCont_TNF_ex2
TPM_for_GEO_upload_COX2.txt

value: HUVECs

value: human umbilical vein endothelial cells

value: wild type


title: SHH-MB_PDX1, THZ1, 16h, rep1

description:
160944_T101_1
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt


title: HNSCC_LMU_KKG_Sample_022


title: sample_025: Intestine from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: NVSel

value: Intestine


title: HNSCC_LMU_KKG_Sample_062


title: si-control-transfeced and TNFα-treated HUVECs no1

description:
siCont_TNF_ex1
TPM_for_GEO_upload_COX2.txt

value: 26 hours


title: sample_024: Kidney from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

source_name: Kidney

value: Kidney


title: SHH-MB_PDX1, JQ1, 16h, rep2

description:
160944_JQ11_2
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

value: 1μM JQ1 treated for 16h


title: SHH-MB_PDX1, JQ1, 16h, rep1

description:
160944_JQ11_1
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt


title: sample_027: Intestine from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: IHNV

value: 4 hrs


title: HNSCC_LMU_KKG_Sample_023

value: head and squamous cell carcinoma


title: sample_022: Kidney from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: si-control-transfected HUVECs no2

description:
siCont_ex2
TPM_for_GEO_upload_COX2.txt

value: control


title: HNSCC_LMU_KKG_Sample_067

value: tumor tissue

value: positive


title: SHH-MB_PDX1, DMSO, 16h, rep1

description:
160944_DMSO_1
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

value: human SHH-subtype medulloblastoma cells

value: 0.1% DMSO treated for 16h


title: sample_020: Kidney from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: HNSCC_LMU_KKG_Sample_065

value: negative


title: sample_023: Kidney from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: SHH-MB_PDX2, Input

data_processing:
ChIP-seq reads were aligned to GRCh38 or GRCm38 reference genome using Bowtie 2 (version 2.3.0).
BAM files were converted by SAMtools (version 1.9).
H3K27ac peaks were called by MACS2 (version 2.2.6) with a q-value threshold of 0.05.
Active enhancers were called by ROSE2 with a stitching distance of 12.5 kb and a transcription start site (TSS) exclusion distance of 2.5 kb.
Super-enhancers were ranked and identified by the Rank Ordering of Super-Enhancers (ROSE) algorithm, and annotated to the closest gene with a certain level of mRNA expression (FPKM > 1).
Assembly: hg38 for Homo sapiens samples, mm10 for Mus musculus samples.
Supplementary files format and content: bigWig

source_name: Cells freshly constructed from SHH-MB_PDX2 xenograft

extract_protocol:
Cell samples were incubated with 1% formaldehyde to crosslink the protein-DNA complexes and subsequently quenched the formaldehyde by adding 125 mM glycine. Samples for ChIP-seq assays were then frozen in liquid nitrogen, and sent to ROMICS company (Shanghai, China) for sonication, chromatin immunoprecipitation, and DNA extraction.
Samples for ChIP-seq assays were sent to ROMICS company (Shanghai, China) for library construction and second-generation sequencing.


title: HNSCC_LMU_KKG_Sample_052

source_name: head and squamous cell carcinoma


title: HNSCC_LMU_KKG_Sample_068


title: SHH-MB_PDX2, H3K27ac, ChIP

value: Cells freshly constructed from SHH-MB_PDX2 xenograft

value: H3K27ac (Active Motif, #39133)


title: HNSCC_LMU_KKG_Sample_051


title: HNSCC_LMU_KKG_Sample_049


title: si-control-transfected HUVECs no3

description:
siCont_ex3
TPM_for_GEO_upload_COX2.txt

value: HUVECs

value: human umbilical vein endothelial cells

value: wild type


title: sample_018: Liver from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

source_name: Liver

value: NVSel

value: 0 hrs

value: Liver


title: SHH-MB_PDX1, Input

source_name: Cells freshly constructed from SHH-MB_PDX1 xenograft


title: sRNA_MT4_HIV_rep2

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

description:
short RNA
HIV-1-infected
sRNAseq_RPKM.txt

data_processing:
TrimGalore-v0.4.1
Mapping: Hisat2-v2.1.0
Read count quantification: Seqmonk-v.1.47.2
Assembly: GRCh38
Supplementary files format and content: txt files containing RPKM expression values of short RNAs (miRNAs, miscRNAs, rRNAs, tRNAs, snRNAs, snoRNAs) and long RNAs (ribosomal-depleted)

source_name: human CD4 + T-cell line MT4 infected with a cell-free HIV-1 strain NL4-3

growth_protocol: MT4 cell line was cultured in RPMI 1640 with L-Glutamine and 25 mM Hepes supplemented with 10% FBS, penicillin (100 U/mL) and streptomycin (100 μg/mL) (all Sigma-Aldrich), under standard conditions at 37 °C under a humidified (>90%) atmosphere of 5% CO2/95% air.

extract_protocol:
MT4 cells infected and uninfected were collected by centrifugation (225× g, 5 min, at 20 °C). Cells pellets were washed with PBS and cells were lysed with RNAzol reagent (Sigma-Aldrich). Virus-containing supernatants were filtered (0.45 μm pore size cellulose-acetate filter (VWR)), and stored at −80 °C. HIV-1 titer was measured by 10-fold serial infection of TZM-bl cells (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH from Dr. John C. Kappes and Dr. Xiaoyun Wu) in triplicate, calculated by Reed-Muench method and expressed as 50% tissue culture infectious dose. Small RNA fraction was purified according to the RNAzol manufacturer’s protocol. The RNA concentration was determined on NanoDrop ONE (ThermoFisher Scientific) and the RNA sample quality control was performed on a 4200 TapeStation System
NAD CaptureSeq: Briefly, only short fraction of RNA from MT4 cells infected by HIV-1 and MT4 cells not infected was used for the library preparation. The most critical step is the enzyme reaction catalyzed by ADP-ribosylcyclase (ADPRC, Sigma-Aldrich), which is an enzyme specific only for NAD-capped RNA but inactive on canonical RNA. Samples not treated by ADPRC were used as a negative control for non-specifically bound RNA. 100 μg of sRNA for each sample was incubated with 4-pentyn-1-ol (10%) and ADPRC (2.5 ug) in 50 mM Na-HEPES (pH 7.0) and 5 mM MgCl2 for 30 min at 37 °C. The reaction was stopped by phenol/ether extraction and RNA was ethanol precipitated. NAD-capped RNA was then biotinylated (biotin-PEG3-azide, 250 mM) via a copper-catalyzed azide-alkyne cycloaddition (CuAAC) in a freshly prepared mixture of CuSO4 (1 mM), THPTA (0.5 mM) and sodium ascorbate (2 mM) for 30 min at 25 °C, with shaking at 350 r.p.m. The biotinylated RNA was purified by phenol/ether extraction and ethanol precipitated. Mobicol Classic columns (MoBiTec, GmbH) were assembled and 50 μl of streptavidin Sepharose (GE Healthcare) was transferred to each column. After washing the beads by adding three times 200 μL of immobilization buffer (10 mM Na-HEPES, 1 M NaCl and 5 mM EDTA, pH 7.2) to each column and centrifuge at ≥16,100 g for 1 min at rt, the beads were blocked with acetylated BSA (100 μg/ml, Sigma-Aldrich) in 100 uL of immobilization buffer for 20 min at 20 °C, with shaking at 1,000 r.p.m. After three more washes, the RNA was immobilized on the beads for 1 h at 20 °C, with shaking at 1,000 r.p.m. The beads were washed five times with 200 μL of streptavidin wash buffer (50 mM Tris-HCl and 8 M urea, pH 7.4), then equilibrated by washing three times with 200 μL of 1x standard ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, pH 7.4), blocked with acetylated BSA, and washed three more times with 1x standard ligation buffer as described previously. 30 μL of ligation mixture containing adenylated RNA 3′adaptor (5 μM, rApp-CNNNNNNAGATCGGAAGAGCACACGTCTG-(C3)), 1x standard ligation buffer, DMSO (15%, Sigma-Aldrich), acetylated BSA (1.5 μg), 2-mercaptoethanol (50 mM, Sigma-Aldrich), T4 RNA ligase (15 U, Thermo Fisher Scientific), and T4 RNA ligase 2, truncated K227Q(300 U, New England BioLabs) was added to the beads and the mixture was incubate at 4 °C overnight (≥16 h). The biotinylated RNA was rebound by adding 7.5 μL 5 M NaCl and incubated for 1 hour at 20 °C, with shaking at 1,000 r.p.m. After washing the beads five times with the streptavidin wash buffer, they were equilibrated by washing three times with 1× first-strand buffer (50 mM Tris-HCl, 75 mM KCl and 5 mM MgCl2, pH 8.3), blocked with acetylated BSA, and washed another three times with 1× first-strand buffer. The beads were covered with 30 μL of reverse transcription mixture containing dNTPs (0.5 mM each,company), acetylated BSA (1,5 μg), DTT (5 mM), 1x first strand buffer, reverse primer (5 uM, CAGACGTGTGCTCTTCCGAT), and Superscript III reverse transcriptase (300 U) and incubated for 1 hour at 37 °C. The rebinding procedure was repeated and samples were washed five times with streptavidin wash buffer and three times with 1x ExoI buffer (Thermo Scientific). The beads were blocked with acetylated BSA in ExoI buffer and again washed three times with 1x ExoI buffer. The free primers were digested by adding 30 μL of 1x ExoI buffer and 30 U of ExoI (Thermo Scientific) and the mixture was incubated for 30 min at 37 °C. The beads were washed five times with streptavidin wash buffer and three times with immobilization buffer. The RNA was digested by adding 100 μl of 0.15 M NaOH solution and incubating for 25 min at 55 °C. The columns were centrifuged and washed with 100 ul of H2O. The flow-through was ethanol precipitated and the cDNA pellet was dissolved in 19 μl of Terminal deoxynucleotidyl transferase (TdT) tailing mixture containing 1x TdT buffer (Thermo Scientific) and CTP (1.25 mM). After adding 20 U of TdT, the mixture was incubated in thermocycler for 30 min at 37 °C and after the enzyme was thermally denatured by heating to 70 °C for 10 min. Then, the second adaptor was ligated on the cDNA by adding 60 μl of reaction mixture containing 1x standard ligation buffer, cDNA anchor (5 μM each strand, sense: p-CAGATCGGAAGAGCGTCGTGT-(C3), antisense: ACACGACGCTCTTCCGATCTGGG), ATP (10 μM), and T4 DNA ligase (120 Weiss U, Thermo Scientific) and incubating for 16 h at 4 °C.PCR amplification was performed with barcoded PCR primers (Table) in 25 cycles inTaq DNA Pol reaction buffer 1 × (Thermo Scientific), with 1 μM of each barcoded primer, 0.2 mM dNTPs (each) and 2.5 U of DreamTaq DNA Polymerase (Thermo Scientific) in 50 μL of total reaction mixture. Initial denaturation was performed at 95 °C for 3 min, following by annealing for 30 s at 68 °C, elongation for 30 s at 72 °C and denaturation for 30 s at 95 °C. Final extension was performed at 72 °C for 5 min. PCR reaction mixture was loaded on 2.5% agarose gel (140 V for 2 h). Fractions between 100–400 nt were cut and DNA was extracted from the gel by Monarch DNA Gel extraction Kit  (NEB). Multiplexed samples were submitted to the IMG Genomics and Bioinformatics facility for library synthesis using the NextSeq® 500/550 High Output Kit v2, 75 cycles (Illumina) and sequencing on a NextSeq 500/550, Illumina. Short RNA-seq: The library synthesis was done using the NEBNext®Small RNA Library Prep Set for Illumina with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-3) and sequenced on a NovaSeq 6000 System (SE 50 bp, 350-400 milions of reads, DS-270). Total RNA-seq: KAPA RNA HyperPrep Kit with RiboErase was used to prepare the libraries and the sequencing was performed using the NextSeq® 500/550 High Output Kit v2, 75 cycles (Illumina) and on a NextSeq 500/550, Illumina.

treatment_protocol: MT4 cells were infected with a cell-free HIV-1 strain NL4-3, which was generated by transient transfection of HEK293T cells with a pNL4-3 plasmid (obtained through NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH from Dr. Malcolm Martin). The infected cultures were subsequently expanded by co-cultivation: 48 h post-infection, cell culture supernatants containing viral particles and infected cells were added to uninfected MT-4 cells (5*105 cells per mL) at a ratio of 1:9. The co-culture was synchronized by three successive additions of infected culture supernatant to uninfected MT-4 cells (5*105 cells per mL, the ratio of 1:9, 27 h interval). The cell cultures were incubated for additional 40 hours and then harvested.

tag: infection

tag: agent

value: no


title: sample_017: Liver from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: IHNV


title: sRNA_MT4_HIV_rep1


title: sRNA_MT4_rep2

description:
short RNA
control
sRNAseq_RPKM.txt

source_name: human CD4 + T-cell line MT4


title: sample_021: Kidney from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: 4 hrs

value: Kidney


title: sRNA_MT4_HIV_rep3


title: Perianal16_Rect_cytoRNA

city: New York

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
Single Cell Process Illumina sequencing products were demultiplexed by the University of Minnesota Genomic Center (UMGC). Prepared FASTQ files were fed into the cellranger count v6.1.1 pipeline for additional QC, alignment, and matrices generation. Filtered matrix outputs were brought into the Seurat wrapper, coreSC, for broad-scope data cleaning and regularization. Gene expression variance stabilization was conducted using the SCTransform v2 function. Normalized GEX outputs were passed to principal component analysis (PCA) and uniform manifold projection (UMAP) for dimensionality reduction and 2-dimensional projection. Individual samples were combined into a single, integrated object and harmonized for batch effects using the Harmony package. Clusters were annotated by parallel data driven and known marker approaches and validated with CellTypist. Clusters classified as myeloid or stromal were subset from the larger Seurat object and sub-clustered.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: MEX compatible cell-associated barcodes list
Supplementary files format and content: MEX compatible gene ID/name list
Supplementary files format and content: MEX format feature-barcode associated UMI count sparse matrix

molecule: cytoplasmic RNA

source_name: rectum biopsies

extract_protocol:
Single Cell Sampling and Isolation  Biopsies for single cell processing were obtained from patients at the time of colonoscopy or upon undergoing abdominoperineal resection (completion proctectomy). At endoscopy, ~4 biopsies per region were collected by the physician for further single cell isolation. From proctectomy specimens, 10-20 biopsies per region were collected by the researcher using an endoscopic forceps prior to pathological grossing. To sample the fistula tract, a cross-section was first excised and then transected to expose the tract lining and facilitate biopsy acquisition. From surgical specimens with patent perianal fistulas, cross sections of the tract were resected with the assistance of the pathologist or pathology PA and preserved in O.C.T. Compound (Sakura) by the Mount Sinai Biorepository Core. FFPE specimens were retrieved from clinical samples previously processed and banked by the Biorepository.  Single cell suspensions were prepared from 4-10 biopsies as previously described21. If cell viability was < 70%, dead cells were depleted using the Dead Cell Removal Kit (Miltenyi, cat.no. 130-090-101). Single cells were loaded onto the 10X Chromium Controller at a targeted concentration of 6000 cells/lane, using the Chromium 3’ v3.1 chemistry (PN-1000121), per manufacturer instructions.
Cells were loaded on a Chromium Next GEM Chip G Single Cell Kit (PN-1000127) with GEMs from the Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000268) and indexed using the Dual Index Kit TT Set A (PN-1000215) according to 10x protocol CG000315 Revs B,C.

value: rectum biopsies

tag: procedure

value: proctectomy


title: si-control-transfected HUVECs no1

description:
siCont_ex1
TPM_for_GEO_upload_COX2.txt

value: control

value: 26 hours


title: HNSCC_LMU_KKG_Sample_047

value: head and squamous cell carcinoma

value: tumor tissue

value: positive


title: HNSCC_LMU_KKG_Sample_045

value: negative


title: sample_015: Liver from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

tag: FISH strain


title: HNSCC_LMU_KKG_Sample_039


title: sample_014: Liver from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

tag: pathogen strain


title: sRNA_MT4_rep3

description:
short RNA
control
sRNAseq_RPKM.txt


title: Perianal16_Fistula_cytoRNA

description: 10x Genomics

source_name: fistula tract lining biopsies

value: fistula tract lining biopsies


title: SHH-MB_PDX1, H3K27ac, ChIP

value: Cells freshly constructed from SHH-MB_PDX1 xenograft

value: human SHH-subtype medulloblastoma cells

value: H3K27ac (Active Motif, #39133)


title: HNSCC_LMU_KKG_Sample_035


title: ZM532, AF, INPUT

city: Chengdu

first: Mao

last: Chen

address: Section 4-13, Renmin Rd. South

institute: Biogas Institute of Ministry of Agriculture and Rural Affairs

data_processing:
The raw sequencing reads of fastq format were first processed by in-house Perl scripts.
Reads were subsequently checked by FastQC (v1.2) before proceeding with downstream processing.
Clean reads were then mapped to Z. mobilis ZM4 reference genome using Bowtie2 and further subjected to peak calling using MACS2.
The mapping results were visualized using the Integrative Genomics Viewer
Assembly: NC_006526.2
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Zymomonas mobilis

growth_protocol: Z. mobilis were grown to an OD600 of 0.6 in RM or AF.

extract_protocol:
Formaldehyde was added to cultures to a final concentration of 1% and cells were crosslinked for 25 min at 30 °C with 100 rpm rotation. Quench formaldehyde was carried out by adding 0.25 M glycine. After crosslink, cells were collected by centrifugation at 4,000 rpm for 10 min and washed twice with 1× ice-cold Phosphate Buffered Saline. The crosslinked pellets were stored at -80 °C until use, or resuspended in 1 ml FA lysis buffer (50 mM Hepes-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) per 50 ml cultures containing 2 mg ml-1 lysozyme and 1× Protease Inhibitor Cocktail II (Abcam), and then incubated at 37 °C for 30 min to lyse cells. Sonication was used to shred genomic DNA into 200-500 bp fragments, which were then centrifuged at 14,000 rpm for 15 min. The supernatant was retained and either used for immunoprecipitation or stored at -80 °C. Before starting the IP assays, ~ 2% of the supernatant was kept as the input sample, and the remaining extract was pre-cleared with 30 μl agarose protein G beads (CST, 9007s) at 4 °C for 1 h to reduce nonspecific background. The beads can be pelleted by centrifuging at 6,000 rpm for 1 min as per manufacturer’s instructions. 4 μg ml-1 anti-Zur or 10 μg ml-1 anti-Fur monoclonal antibody was added to the supernatant above and incubated at 4 °C overnight. After that, 30 μl agarose protein G beads were added and rocked at 4 °C for 1 h. After centrifugation, the beads were washed twice with 1 ml FA lysis buffer, once with high salt buffer (lysis buffer + 500 mM NaCl), once with LiCl buffer (10 mM Tris, pH 7.5, 1 mM EDTA, 250 mM LiCl, 0.5 % Na deoxycholate), and twice with TE buffer (10 mM Tris, pH 7.5, 1 mM EDTA). Finally, the beads were incubated with 100 μl elution buffer (50 mM Tris, pH 7.5, 10 mM EDTA, 1% SDS) for 20 min at 65 °C and washed once with 150 μl of TE + 0.67% SDS. The supernatant of eluted DNA complexes above was collected and then blended. In addition, 150 μl of TE + 0.67% SDS was added to the input sample. To reverse the crosslinking, all IP and input samples were incubated at 65 °C overnight. After treated with 1 μl of RNase A (10 mg ml-1) and 5 μl of Proteinase K (10 mg ml-1) at 37 °C for 1 h respectively, the immunoprecipitated chromatin was purified using phenol-chloroform-isoamyl alcohol method and resuspend in 50 μl TE buffer pH 7.5.
The DNA-sequencing library was generated by NEBNext Ultra II DNA Library Prep Kit (NEB) as per manufacturer’s instructions and subsequently sequenced on the Illumina HiSeq X Ten platform in 150PE mode.

tag: strain


title: sample_013: Liver from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using fqC v0.11.5 and TrimGalore! software v0.6.4_dev. This software was used to trim low-quality ends from reads, for Illumina adapter removal, and for removal of excess poly(A)-tails.
STAR v2.7.7a was used for alignment of reads to the rainbow trout genome using the default alignment parameters recommended by the STAR software.
Gene counts for reverse-stranded preparations were provided by STAR v2.7.7a using default parameters recommended by the STAR software.
Read counts output from the STAR v2.7.7a software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-BiocManager Release 1.30.10.
Genome_build: All unmasked sequences from the rainbow trout primary assembly in Ensemble (Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly)
Supplementary_files_format_and_content: Tab-delimited text files of effective read counts, rounded to the nearest whole number

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly-A selected kit with 200-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input. Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer. The RNA integrity was checked by Agilent Bioanalyzer 2100 and samples with clean rRNA peaks were used for further experiments.
RNA-Seq of 150 bp PE (paired end) reads were sequenced on Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).

value: NVSel

tag: time post pathogen challenge

value: 0 hrs

value: Liver


title: NK_D4_R

city: Ramat Gan

first: Tirza

middle: T

last: Doniger

state: Not US or Canada

address: Bar Ilan University

department: The Mina and Everard Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

data_processing:
The RNA sequencing data was trimmed using Trim_galore (version 0.5.0) and aligned using STAR (v2.7.3a)  with default parameters. The ENSEMBL human hg38 build and its corresponding GTF were used to build the STAR reference database. The number of reads per gene was quantified using HTSeq-Count (v0.6.1p1).
Assembly: hg38
Supplementary files format and content: tab-delimited file with gene name and raw counts

source_name: PBMC

extract_protocol:
Primary NK cells after sorting were processed for RNA isolation. Isolation was performed based on the Quick-RNA Microprep (Cat no. R1050 & R1051; ZymoResearch) according to the manufacturers’ protocol.
RNA libraries were prepared using Illumina Stranded RNA Kit following manufacter's protocols.

value: PBMC

tag: subject

value: primary NK cells

tag: disease state

value: healthy

tag: cell population

value: Responsive


title: ZM532, AF, Zur, rep2

value: anti-Zur


title: NK_D4_A

value: Anergic


title: HNSCC_LMU_KKG_Sample_030

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: tab-delimited text file with filtered raw counts

extract_protocol:
Simultaneous DNA and total RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD using unique dual indexing

value: head and squamous cell carcinoma

tag: hpv-status

tag: mps-all

tag: mps-hpv negative


title: HNSCC_LMU_KKG_Sample_025

value: tumor tissue


title: sample_016: Liver from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

city: Auburn

first: Jason

last: Abernathy

address: 990 Wire Road

institute: USDA-ARS

value: IHNV


title: sample_012: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: Intestine


title: ZM532, AF, Zur, rep1

tag: chip antibody


title: sample_011: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sRNA_MT4_rep1

description:
short RNA
control
sRNAseq_RPKM.txt

value: no


title: ZM532, AF, Fur, rep2

value: anti-Fur


title: NK_D3_A


title: HNSCC_LMU_KKG_Sample_024

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

institute: LMU University Hospital

value: negative


title: sample_010: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_016

value: positive


title: sample_009: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: NVSel


title: NK_D2_R


title: NK_D2_A


title: ZM532, AF, Fur, rep1


title: zurfur, KO, RM, rna-seq, rep3

data_processing:
The raw sequencing data was first subjected to quality control using FraserQC (v1.2) with the default parameters.
Reads were then aligned to Z. mobilis ZM4 reference genome using Bowtie2.
Genes expression levels were quantified by featureCounts of Subread package.
Differentially expressed genes (DEGs) were screened according to the criteria of Foldchange ≥ 2 and FDR < 0.05 by DESeq2. GO enrichment of DEGs was analyzed by clusterProfiler.
Assembly: NC_006526.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using the trizol method and checked on an agarose gel to monitor the degradation and contamination. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent).
Sequencing libraries were generated from 1 μg total RNA per sample using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

tag: genotype

value: zur and fur knockout

tag: treatment

value: RM


title: NK_D1_R

tag: tissue

value: PBMC

tag: cell type


title: HNSCC_LMU_KKG_Sample_007


title: NK_D1_A

value: primary NK cells


title: zurfur, KO, RM, rna-seq, rep1


title: sample_007: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: 0 hrs


title: HNSCC_LMU_KKG_Sample_002


title: NK_D3_R

value: healthy

value: Responsive


title: zurfur, KO, RM, rna-seq, rep2


title: MT4 +ADPRC +HIV rep4

data_processing:
Library strategy: NAD captureSeq
Trimming:  TrimGalore-v0.4.1
Mapping:  Hisat2-v2.1.0
Read count quantification:  Seqmonk-v.1.47.2
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file containing raw read counts of short RNAs (miRNAs, miscRNAs, rRNAs, tRNAs, snRNAs, snoRNAs)

extract_protocol:
MT4 cells infected and uninfected were collected by centrifugation (225× g, 5 min, at 20 °C). Cells pellets were washed with PBS and cells were lysed with RNAzol reagent (Sigma-Aldrich). Virus-containing supernatants were filtered (0.45 μm pore size cellulose-acetate filter (VWR)), and stored at −80 °C. HIV-1 titer was measured by 10-fold serial infection of TZM-bl cells (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH from Dr. John C. Kappes and Dr. Xiaoyun Wu) in triplicate, calculated by Reed-Muench method and expressed as 50% tissue culture infectious dose. Small RNA fraction was purified according to the RNAzol manufacturer’s protocol. The RNA concentration was determined on NanoDrop ONE (ThermoFisher Scientific) and the RNA sample quality control was performed on a 4200 TapeStation System
Briefly, only short fraction of RNA from MT4 cells infected by HIV-1 and MT4 cells not infected was used for the library preparation. The most critical step is the enzyme reaction catalyzed by ADP-ribosylcyclase (ADPRC, Sigma-Aldrich), which is an enzyme specific only for NAD-capped RNA but inactive on canonical RNA. Samples not treated by ADPRC were used as a negative control for non-specifically bound RNA. 100 μg of sRNA for each sample was incubated with 4-pentyn-1-ol (10%) and ADPRC (2.5 ug) in 50 mM Na-HEPES (pH 7.0) and 5 mM MgCl2 for 30 min at 37 °C. The reaction was stopped by phenol/ether extraction and RNA was ethanol precipitated. NAD-capped RNA was then biotinylated (biotin-PEG3-azide, 250 mM) via a copper-catalyzed azide-alkyne cycloaddition (CuAAC) in a freshly prepared mixture of CuSO4 (1 mM), THPTA (0.5 mM) and sodium ascorbate (2 mM) for 30 min at 25 °C, with shaking at 350 r.p.m. The biotinylated RNA was purified by phenol/ether extraction and ethanol precipitated. Mobicol Classic columns (MoBiTec, GmbH) were assembled and 50 μl of streptavidin Sepharose (GE Healthcare) was transferred to each column. After washing the beads by adding three times 200 μL of immobilization buffer (10 mM Na-HEPES, 1 M NaCl and 5 mM EDTA, pH 7.2) to each column and centrifuge at ≥16,100 g for 1 min at rt, the beads were blocked with acetylated BSA (100 μg/ml, Sigma-Aldrich) in 100 uL of immobilization buffer for 20 min at 20 °C, with shaking at 1,000 r.p.m. After three more washes, the RNA was immobilized on the beads for 1 h at 20 °C, with shaking at 1,000 r.p.m. The beads were washed five times with 200 μL of streptavidin wash buffer (50 mM Tris-HCl and 8 M urea, pH 7.4), then equilibrated by washing three times with 200 μL of 1x standard ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, pH 7.4), blocked with acetylated BSA, and washed three more times with 1x standard ligation buffer as described previously. 30 μL of ligation mixture containing adenylated RNA 3′adaptor (5 μM, rApp-CNNNNNNAGATCGGAAGAGCACACGTCTG-(C3)), 1x standard ligation buffer, DMSO (15%, Sigma-Aldrich), acetylated BSA (1.5 μg), 2-mercaptoethanol (50 mM, Sigma-Aldrich), T4 RNA ligase (15 U, Thermo Fisher Scientific), and T4 RNA ligase 2, truncated K227Q(300 U, New England BioLabs) was added to the beads and the mixture was incubate at 4 °C overnight (≥16 h). The biotinylated RNA was rebound by adding 7.5 μL 5 M NaCl and incubated for 1 hour at 20 °C, with shaking at 1,000 r.p.m. After washing the beads five times with the streptavidin wash buffer, they were equilibrated by washing three times with 1× first-strand buffer (50 mM Tris-HCl, 75 mM KCl and 5 mM MgCl2, pH 8.3), blocked with acetylated BSA, and washed another three times with 1× first-strand buffer. The beads were covered with 30 μL of reverse transcription mixture containing dNTPs (0.5 mM each,company), acetylated BSA (1,5 μg), DTT (5 mM), 1x first strand buffer, reverse primer (5 uM, CAGACGTGTGCTCTTCCGAT), and Superscript III reverse transcriptase (300 U) and incubated for 1 hour at 37 °C. The rebinding procedure was repeated and samples were washed five times with streptavidin wash buffer and three times with 1x ExoI buffer (Thermo Scientific). The beads were blocked with acetylated BSA in ExoI buffer and again washed three times with 1x ExoI buffer. The free primers were digested by adding 30 μL of 1x ExoI buffer and 30 U of ExoI (Thermo Scientific) and the mixture was incubated for 30 min at 37 °C. The beads were washed five times with streptavidin wash buffer and three times with immobilization buffer. The RNA was digested by adding 100 μl of 0.15 M NaOH solution and incubating for 25 min at 55 °C. The columns were centrifuged and washed with 100 ul of H2O. The flow-through was ethanol precipitated and the cDNA pellet was dissolved in 19 μl of Terminal deoxynucleotidyl transferase (TdT) tailing mixture containing 1x TdT buffer (Thermo Scientific) and CTP (1.25 mM). After adding 20 U of TdT, the mixture was incubated in thermocycler for 30 min at 37 °C and after the enzyme was thermally denatured by heating to 70 °C for 10 min. Then, the second adaptor was ligated on the cDNA by adding 60 μl of reaction mixture containing 1x standard ligation buffer, cDNA anchor (5 μM each strand, sense: p-CAGATCGGAAGAGCGTCGTGT-(C3), antisense: ACACGACGCTCTTCCGATCTGGG), ATP (10 μM), and T4 DNA ligase (120 Weiss U, Thermo Scientific) and incubating for 16 h at 4 °C.PCR amplification was performed with barcoded PCR primers (Table) in 25 cycles inTaq DNA Pol reaction buffer 1 × (Thermo Scientific), with 1 μM of each barcoded primer, 0.2 mM dNTPs (each) and 2.5 U of DreamTaq DNA Polymerase (Thermo Scientific) in 50 μL of total reaction mixture. Initial denaturation was performed at 95 °C for 3 min, following by annealing for 30 s at 68 °C, elongation for 30 s at 72 °C and denaturation for 30 s at 95 °C. Final extension was performed at 72 °C for 5 min. PCR reaction mixture was loaded on 2.5% agarose gel (140 V for 2 h). Fractions between 100–400 nt were cut and DNA was extracted from the gel by Monarch DNA Gel extraction Kit  (NEB). Multiplexed samples were submitted to the IMG Genomics and Bioinformatics facility for library synthesis using the NextSeq® 500/550 High Output Kit v2, 75 cycles (Illumina) and sequencing on a NextSeq 500/550, Illumina.
NADcapture shortRNA seq

tag: cell line

value: CD4 + T-cell

tag: infection

value: ADPRC

tag: sample type

value: NAD-capped RNA

tag: rna fraction

value: short RNA


title: MT4 +ADPRC +HIV rep3


title: sample_005: Kidney from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

tag: FISH strain

tag: pathogen strain

value: IHNV

value: Kidney


title: zur, KO, RM, rna-seq, rep2

tag: strain

value: zur knockout


title: HNSCC_LMU_KKG_Sample_034

value: head and squamous cell carcinoma

value: tumor tissue

value: negative


title: sample_004: Kidney from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: NVSel

tag: time post pathogen challenge


title: MT4 +ADPRC +HIV rep2


title: sample_008: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: Intestine


title: ZM532, AF, rna-seq, rep3

value: Genomic mutants

value: Acetic acid and furfural


title: zur, KO, RM, rna-seq, rep1

value: RM


title: sample_003: Kidney from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: 0 hrs


title: MT4 +ADPRC +HIV rep1


title: sample_002: Kidney from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: HNSCC_LMU_KKG_Sample_092


title: LP, SV, scRNA-seq

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation Street

department: BMB

institute: Umass Chan Medical School

description: 10x Genomics

data_processing:
Seurat was used for clustering single-cell data. We filtered cells that have a number of unique features (genes) less than 500, a number of unique molecular identifiers (UMI) less than 200, and a percentage of mitochondrial genes over 1%. After filtering, we have total 47,804 cells and 19,601 features (genes) with average 6053 UMI per cell. Filtered data was normalized with SCTransform as described in {Choudhary, 2022 #3428}. Transformed data across conditions were then integrated with canonical correlation analysis. Genes from the FindVariableFeatures function were used as input for the initial principal component analysis (PCA). The number of principal components (PCs) was chosen based on the Seurat ElbowPlot function. We set resolution parameters from 0.1 to 1.4 and examined the clustering quality based on DoHeatmap function and clustree. We identified significantly differentially expressed markers in each cluster by running the default FindAllMarkers function. We annotated cell types based on well-established markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and mitrix files.

source_name: Seminal vesicle

extract_protocol:
After euthanizing the mice, the urogenital system was exposed. The entire urogenital system was taken out of the mouse abdominal cavity and placed into a 60 mm Petri dish containing 5 ml complete medium (CM) composed of IMDM (Invitrogen), 10% FBS (Sigma), and Antibotica-Antimycotic (invitrogen). Under a dissection microscope, carefully remove the surrounding organs and tissues. Open the seminal vesicle longitudinally with a scissor and let seminal vesicle fluid out of the organ. Transfer the tissue to another dish and gently remove any loose coagulated seminal vesicle fluid without disturbing the epithelial cell layer.  After washing, the tissue was transferred into a 15 ml conical tube with 2 ml CM and 2 ml extracellular matrix digestion media (ECM) containing collagenase (Sigma), DNase (Sigma), collagenase/hyaluronidase (Stem Cell), and collagenase/dispase (Sigma). The tissue was incubated in a water bath at 300 rpm for 30 minutes at 35 C. After incubation, 10 ml IMDM-DNase media was added to the tube and centrifuged at 300 g for 5 minutes at room temperature. Wash the pellet once with 8 ml IMDM-DNase media. Resuspend the pellet with 3 ml TrypLEtm express (Gibco), and digested the tissue in the water bath at 300 rpm for 5 minutes at 35 C. Fill the tube with 10 ml CM and filter the cell suspension through a series of 100 μm, 70 μm, and 40 μm cell strainers. Pellet the cells by centrifuging for 5 minutes at 300 g. Resuspend the pellet with 3 ml CM. The cell suspension was then placed on the top of OptitPrep (Sigma) gradient followed by centrifuging at 800 g for 15 minutes. The gradient was composed of 3 ml of 67%, 50%, and 36% OptiPrep in CM, respectively. Interface fractions were collected and cells were pelleted, washed 1X with CM, and resuspended in 1 ml CM. The samples with cell viability over 80% were used for sequencing library preparation.
Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics), as per the manual.

treatment_protocol: Mice were housed under a controlled lighting regimen (12-h light: 12 h dark) at 21 to 22 °C and supplied with food and water ad libitum.

value: Seminal vesicle

tag: Sex

value: male

value: FVB/NJ

value: Wild type

value: diet


title: MT4 -ADPRC +HIV rep4

value: CD4 + T-cell

value: no ADPRC

value: control

value: short RNA


title: HNSCC_LMU_KKG_Sample_013

value: head and squamous cell carcinoma

value: tumor tissue

tag: hpv-status


title: sample_006: Kidney from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: NVSel

value: IHNV

value: Kidney


title: ZM532, AF, rna-seq, rep2

value: Genomic mutants

value: Acetic acid and furfural


title: Con, SV, scRNA-seq

description: 10x Genomics


title: HF, SV, scRNA-seq

description: 10x Genomics


title: zur, KO, RM, rna-seq, rep3

value: zur knockout

value: RM


title: sample_001: Kidney from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: 0 hrs


title: SMB56, GDC-0449, 8h, in vitro, rep2

description:
R20-2-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: mouse SHH-subtype medulloblastoma cells

value: 1μM GDC-0449 treated for 8h


title: Old, SV, scRNA-seq

description: 10x Genomics

value: Seminal vesicle

value: male

value: FVB/NJ

value: Wild type

value: aging


title: ZM532, AF, rna-seq, rep1


title: MT4 -ADPRC +HIV rep2

value: CD4 + T-cell

value: no ADPRC

value: control

value: short RNA


title: ZM532, RM, rna-seq, rep3


title: MT4 -ADPRC +HIV rep1


title: SMB56, GDC-0449, 8h, in vitro, rep1

description:
R20-2-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: Yong, SV, scRNA-seq

description: 10x Genomics


title: SMB56, THZ1, 8h, in vitro, rep2

description:
R18-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: 0.1μM THZ1 treated for 8h


title: MT4 +ADPRC -HIV rep4

value: no HIV-1

value: ADPRC

value: NAD-capped RNA


title: SMB56, THZ1, 8h, in vitro, rep1

description:
R18-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: ZM4, RM, rna-seq, rep3

value: WT

value: RM


title: MT4 +ADPRC -HIV rep2


title: ZM532, RM, rna-seq, rep1

value: Genomic mutants


title: MT4 +ADPRC -HIV rep3


title: ISRH-seq_CK(salt)_rep2

city: Nanjing

first: Wu

last: Jing

address: No.1 Weigang, Nanjing, Jiangsu

institute: Nanjing Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequences using Fastp
Bowtie2（version 2.2.5）was used for aligning clean reads to the rice reference genome (MSU version7.0) with default parameters
R-loop peak calling was performed using MACS2 (version 2.1.4)
Assembly: MSU v7.0
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: ISRH-seq

organism: Oryza sativa

source_name: seeding

growth_protocol: spread into nutrient soil in the pot or hydroponics for 150 mM NaCl treatment for continuing to grow in the greenhouse at 28-30°C and 14 h/10 h light-dark cycle

extract_protocol:
Purified genomic DNA was fragmented into size as 200-500bp using a sonicator. 100ng, 250ng, 500ng, 3 µg, 5 µg and 8 µg fragmented DNA was used for RNase H in combination with DNA polymerase I for in situ labeling with a total 200 µl reaction at 16℃ for 2h
Streptavidin bound biotin labeled DNA strand was used for single-stranded DNA library preparation using scale ssDNA-seq Lib Prep Kit for Illumina V2 (RK20228, ABclonal Technology, China)

value: seeding

value: three-day-salt treated


title: SMB56, JQ1, 8h, in vitro, rep2

description:
R19-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: mouse SHH-subtype medulloblastoma cells

value: 1μM JQ1 treated for 8h


title: SMB56, JQ1, 8h, in vitro, rep1

description:
R19-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: ZM4, RM, rna-seq, rep2


title: MT4 -ADPRC +HIV rep3


title: MT4 +ADPRC -HIV rep1


title: MT4 -ADPRC -HIV rep4


title: ZM4, RM, rna-seq, rep1


title: SMB56, DMSO, 8h, in vitro, rep2

description:
R17-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: 0.1% DMSO treated for 8h


title: zurfur, RM, rep2

description:
Hi-C_zurfur_RM_10k.heatmap_ICed.matrix
Hi-C_zurfur_RM_5kb_heatmap.mcool

data_processing:
The Hi-C raw data generated from the Hi-C library were quality filtered using Trimmomatic v0.3882 and the clean data from two replicates were iteratively mapped to the reference genome Z. mobilis ZM4 (https://www.ncbi.nlm.nih.gov/nuccore/NC_006526.2) using the ICE software package.
Dangling ends and other unusable data were filtered, the valid pairs were used to analyze the correlation efficiency of the two biological replicates for each sample using GenomeDISCO. The valid pairs after pooling were binned into 10 kb, 5 kb, or 2 kb nonoverlapping genomic intervals to generate contact maps.
An insulation score algorithm was used to identify the CID boundaries of each sample, as well as the location and numbers of CIDs.
The bacterial chromosome was binned at 5 kb, and the intra-chromosome contacts of each sample were transferred to Fit-Hi-C software. Significant interactions were identified when both the both the p-value and q-value (false discovery rate, FDR) were less than 0.01 and contact count was greater than 2.
Assembly: NC_006526.2
Supplementary files format and content: Contact matrix

source_name: zurfur

growth_protocol: Z. mobilis strains were cultured to exponential phase and 10^6 cells were collected by centrifugation at 2,000 g and washed with TE.

extract_protocol:
Cells were then crosslinked with 3% fresh formaldehyde for 30 min at room temperature, followed by 30 min at 4 °C. Formaldehyde was finally quenched with 0.375 M glycine for 20 minutes at 4 °C. Fixed cells were collected, frozen in liquid nitrogen, and stored at -80 °C until use. 1 × 10^9 cells were suspended in 100 μl TE with 2 μl of Ready-Lyse lysozyme (Epicentre), and incubated at room temperature for 20 min before being treated with 0.5% SDS treatment for 10 min at 65 °C. SDS was quenched by adding 50 μl 10% Triton X-100 and incubating it for 15 min at 37 °C. The chromosomal DNA in the cell lysate was then digested for 1 h at 37 °C by adding 50 μl 10x NEB buffer 2.1(NEB), 300μl water, and 100U of Sau3AI. Biotin-14-dCTP (TriLINK) was used to label the restriction fragment ends with biotinylated cytosine nucleotides. Labeled DNA was diluted in a 10.0 ml ligation mix containing 100 Weiss units of T4 DNA ligase (Thermo) and ligated overnight at 16 °C. The crosslinking was reversed overnight at 65°C with 200 μg ml-1 proteinase K (Thermo), and DNA was purified using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. Purified DNA was sheared to a length of ~400 bp.
Biotinylated DNA fragments were pulled down by Dynabeads MyOne Streptavidin C1 beads (Thermo fisher) and prepared for Illumina sequencing by NEBNext Ultra II DNA Library Prep Kit (NEB) as per manufacturer’s instructions. The DNA fragments between 400 and 600 bp were purified and paired-end sequenced on the Illumina HiSeq X Ten platform with 150PE mode.

value: zurfur


title: SMB56, DMSO, 8h, in vitro, rep1

description:
R17-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: MT4 -ADPRC -HIV rep3

value: CD4 + T-cell


title: zurfur, RM, rep1


title: Med23KO-3

first: Lu

last: CHENGJIANG

state: China, Mainland

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
The raw reads were assessed with FastQC
The adapter sequences were trimmed with Cutadapt
The trimmed reads were mapped to the mm10 genome with STAR
The RNA expression levels were quantified using FPKM.
Differential gene expression analysis was conducted with cuffdiff
Assembly: mm10
Supplementary files format and content: WT-and-MED23-KO-MuSCs-RNA-seq-3-days-culture.txt

source_name: skeletal muscle

growth_protocol: FACS-sorted MuSCs were cultured in F10 growth medium (20% FBS, 1% penicillin‒streptomycin (P/S), and 5 ng/ml bFGF (PeproTech #100-18B)) on a type I collagen (Corning #354236)-coated dish

extract_protocol:
RNA extraction by the TRIzol-chloroform-ethanol method
The poly (A) RNA were enriched with oligo (dT) beads and subjected to construct strand-specific DNA libraries using an NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

value: skeletal muscle

value: primary muscle stem cells


title: MT4 -ADPRC -HIV rep2

value: no ADPRC

value: control

value: short RNA